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Encyclopedia of microbe genomes: Chapter 1

Genome scientists from the US and Germany have assembled the first pages of a comprehensive encyclopedia of genomes of all the microbes on Earth. The results, published Dec. 24 in the journal Nature, will help biologists find new genes and fill out the branches of the “Tree of Life.”

“This is a rich sampling of the diversity of microbial genomes,” said Professor Jonathan Eisen of the UC Davis Genome Center and the U.S. Department of Energy Joint Genome Institute, and senior author on the paper. “Better sampling across the tree of life gives you better reference points for predicting the functions of genes.”

There are estimated to be a nonillion — 1 followed by 30 zeroes — prokaryotic microbes on the planet. Unlike eukaryotic organisms such as people, yeast and oak trees, the cells of prokaryotes have no membrane wrapped around their DNA. They are divided into two major groups: Bacteria, including a tiny minority that make people sick, and the Archaea, which include organisms that can survive in extreme environments such as hot springs.

About a thousand prokaryote genomes have been sequenced to date, most of them among the small number that cause disease, or that do interesting things such as producing biofuels.

“That's like making a map of the world and only mapping three cities,” Eisen said.

The new study, called the Genomic Encyclopedia of Bacteria and Archaea or GEBA, looks instead at representatives from across the major branches of the family tree of microorganisms. The paper describes the first 56 genomes from this set.

The study shows that although microbes are known to swap genes with other species (a process called “lateral transfer,”) phylogeny, or position on the family tree, is more important in determining where new genes appear and how they spread.

“Lateral transfer does not shuffle evolutionary innovations in a massive way,” Eisen said. “If there is an innovation in a branch, you tend to find it in the same branch downstream.”

The survey also turned up some novel findings, including the first actin in bacteria. Actin is a protein that forms a structural framework inside all eukaryotic cells, allowing cells to crawl and to arrange and move items around internally. Previously, the protein had been thought to exist only in eukaryotic cells. The survey found a structurally similar molecule in the marine bacterium Haliangium ochraceum. The authors hypothesize that the bacterium may use the actin-like protein to make a toxin that attacks other cells.

H. ochraceum also contains hundreds of DNA repeats called CRISPR units. CRISPR is a recently discovered “immune system” that protects bacteria from viruses and other foreign DNA. The CRISPR array in H. ochraceum is by far the largest yet found.

The microbes for the study were grown by a team lead by Hans-Peter Klenk of the German Collection of Microorganisms and Cell Cultures (also known as the DSMZ).

“The GEBA project perfectly fits with our vision for the future of microbial taxonomy and the collection of type strains in general,” Klenk said. The German collection will provide the scientific community with access to the strains used in the project without strings, he said.

The collaborators now plan to add more genomes to their tree. Another 1,500 genomes would cover half the diversity among microbes that can be grown in the lab, Eisen said.

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Eisen also holds appointments at the UC Davis Department of Evolution and Ecology and the Department of Medical Microbiology and Immunology.

Genome sequencing, annotation, and analysis were done primarily at the Joint Genome Institute in Walnut Creek, Calif. Other authors include UC Davis' Dongying Wu, a project scientist in Eisen's lab; Mitchell Singer, professor of microbiology at UC Davis; and multiple collaborators from JGI, DSMZ, the Lawrence Livermore National Laboratory and the University of Virginia, Charlottesville.

The project was funded primarily by the U.S. Department of Energy with support from the Gordon and Betty Moore Foundation and the DSMZ.